seurobj <- readRDS('output/10x-180831')

PC2 seems to capture the difference between Monocle states.

How are some of the branch-dependent genes expressed? Brown genes

White genes

Expression of brown branch genes in the t-SNE

Some of the white branch genes

FeaturePlot(seurobj, features.plot=c('APOD', 'MGP', 'DCN', 'PLAC9', 'IGF2', 'ZFP36', 'FOS',
'TCEAL4',
'C1R',
'OSR2',
'MFGE8',
'FBLN1',
'CLU'), reduction.use='tsne', cols.use=c('gray', 'blue'), no.legend=F, nCol=2)

PC2 heatmap

PCHeatmap(seurobj, pc.use=2, cells.use=100, do.balanced = T, num.genes = 100)

Discrepancy: Rowv is FALSE, while dendrogram is `both'. Omitting row dendogram.Discrepancy: Colv is FALSE, while dendrogram is `column'. Omitting column dendogram.

FeaturePlot(seurobj, features.plot=c('ADIPOQ', 'LIPE', 'PLIN4', 'FASN', 'AGPAT2', 'PCK1', 'MMP2', 'PPAP2B', 'SCARA5', 'IGFBP6', 'SERPING1'), reduction.use='tsne', cols.use=c('gray', 'blue'), no.legend=F, nCol=2)

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